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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/alignment_track.cpp Source File

DECLARE_EVENT_TABLE()

cut_off = m_MaxAlignShownAdaptive;

cut_off = m_MaxAlignShownAdaptive;

cut_off = m_MaxAlignShownFull;

(

<<

<< layout <<

);

(iter.second == layout) {

(iter != sm_LabelPosMap.end()) {

(iter = sm_LabelPosMap.begin(); iter != sm_LabelPosMap.end(); ++iter) {

(iter->second == pos) {

(iter != sm_HideSraMap.end()) {

(iter = sm_HideSraMap.begin(); iter != sm_HideSraMap.end(); ++iter) {

(iter->second == hideSra) {

(iter != sm_UnalignedTailsModeMap.end()) {

(iter = sm_UnalignedTailsModeMap.begin(); iter != sm_UnalignedTailsModeMap.end(); ++iter) {

(iter->second == tailsMode) {

=

;

);

, m_Layout(eLayout_Default)

, m_ShowAlignedSeqFeats(

)

, m_ShowLabel(

)

, m_ShowUnalignedTailsForTrans2GenomicAln(

)

, m_ShowAlnStat(

)

, m_ShowIdenticalBases(

)

, m_ShowSecondPassAlignments(

)

, m_CompactEnabled(

)

, m_CompactThreshold(100)

, m_ExtremeCompactThreshold(1000)

,

));

,

));

,

));

,

));

}

(exception& e) {

title =

;

(preset_style.empty() || preset_style ==

) {

memory_limit = view.

(

,

);

=

->GetData().GetStr();

(list<string>, iter, toks)

<<

<< e.

());

graph_params->

= size_view.GetInt(

, 45);

(

(iter->first,

))

(height >= 10 && graph_params) {

( !toks.empty() ) {

(list<string>, f_iter, toks) {

<<

<< e.

());

(

<<

<< iter->first <<

<< iter->second);

( !preset_style.empty() ) {

settings[

] = preset_style;

settings[

] =

( !projected_feats.empty() ) {

settings[

] = projected_feats;

align_cost = -1;

show_coverage = !sequence_level;

(show_pileup_cache) {

show_coverage =

;

show_aligns =

;

kMaxRegulatAlignmentRows = 1000;

align_limit = kMaxRegulatAlignmentRows;

(

<<

);

(

->m_Token) {

item = menu.AppendCheckItem(

+ curr_id++,

(

));

(

));

(

));

item = menu.AppendCheckItem(

+ curr_id++,

(

));

item = menu.AppendCheckItem(

+ curr_id++,

(

));

item = menu.AppendCheckItem(

+ curr_id++,

(

));

(

));

menu.AppendSeparator();

id_base = 10000;

wxMenuItem* item = menu.AppendRadioItem(id_base + iter.first,

(iter.second + (l_default ?

:

)));

menu.AppendSeparator();

wxMenuItem* item = menu.AppendCheckItem(compact_item_idx,

(

));

wxMenuItemList& item_list = menu.GetMenuItems();

(wxMenuItemList, iter, item_list) {

((*iter)->GetId() == compact_item_idx) {

((*iter)->IsChecked() &&

!=

) {

id_base = 10000;

wxMenuItem* item = menu.AppendRadioItem(id_base + curr_id,

(curr_method == (*iter)->GetName()) {

wxMenuItem* item = menu.AppendRadioItem(id_base + curr_id,

(curr_method == score_name) {

wxMenuItem* item = menu.AppendRadioItem(id_base + curr_id,

(

));

wxMenuItemList& item_list = menu.GetMenuItems();

(wxMenuItemList, iter, item_list) {

checked_id = (*iter)->GetId() - id_base;

((*iter)->IsChecked() && score_id != checked_id) {

(checked_id == curr_id) {

(dlg.ShowModal() == wxID_OK) {

id_base = 10000;

wxMenuItem* items[3];

items[0] = menu.AppendRadioItem(id_base + curr_id++,

,

);

items[1] = menu.AppendRadioItem(id_base + curr_id++,

,

);

items[2] = menu.AppendRadioItem(id_base + curr_id++,

,

);

menu.AppendSeparator();

wxMenuItem* itemTrans2Genomic = menu.AppendCheckItem(

+ curr_id++,

(

));

itemTrans2Genomic->Check();

(items[1]->IsChecked())

(items[2]->IsChecked())

update =

;

vector<CLayoutGroup*> groups;

groups.push_back(curr_group);

groups.push_back(p_group);

first_group =

*

(

.m_ObjectList.front().GetPointer());

p_group = group.GetPointer();

vector< CRef<CAlignGlyph> > aligns;

vector<CLayoutGroup*> groups;

groups.push_back(curr_group);

groups.push_back(p_group);

scored_alns.emplace_back(

);

(project_feats) {

scored_alns.emplace_back(

);

(*mp_iter)->SetRenderingContext(

);

stat_aligns.emplace_back(&(*mp_iter)->GetAlignMgr());

(show_score && (*mp_iter)->GetAlignMgr().IsColoringAvailable()) {

((*mp_iter)->IsSimplified()) {

(*mp_iter)->SetShowScore();

scored_alns.emplace_back(mp_iter->GetPointer());

coverage_annot;

(

);

min_dist = 4.0;

( !aligns.empty() ) {

( !scored_alns.empty() ) {

coverage_annot;

(

.m_ObjectList.empty()) {

(

);

coverage_annot;

(conf_mgr->HasSettings(coverage_annot)) {

params = conf_mgr->GetHistParams(coverage_annot);

conf_mgr->AddSettings(coverage_annot, params);

vector<CAlnStatGlyph*> stat_glyphs;

(

&& ch : objs) {

stat_glyphs.push_back(stat_glyph);

(stat_glyphs.empty()) {

(

&& stat_glyph : stat_glyphs) {

stat_glyph->SetConfig(

, graph_params);

*

((*a_iter)->m_Owner.GetPointer());

(objs.empty() || !align)

;

parent_group->

(align, group);

parent_group->

(align);

group->PushBack(align);

(objs.size() > 1) {

TFeatGroups feat_groups;

feat_groups[s_type].push_back(*iter);

(iter->second.size() > 1) {

group->PushBack(sub_group);

,

,

(0.5, 0.5f, 0.5f, 0.5f),

sub_group->

(iter->second);

group->Append(iter->second);

group->Append(objs);

,

,

(0.0, 0.6f, 0.0f, 0.1f),

group->SetShowGene(

);

group->SetLayoutPolicy(

);

(seq_id.

(*

))

( !conf || !conf->

) {

=

;

(s_ALnTypeMap.count(align_type) != 0)

s_ALnTypeMap[align_type];

(s_AlnLoaderMap.count(align_loader) != 0)

s_AlnLoaderMap[align_loader];

=

;

p_areas->push_back(area);

area->m_ID =

();

(cgi_mode &&

().IsPrinterFriendly() ==

) {

( !src_annots.

() ) {

(track_settings.count(

) > 0) {

vector<string> target_g_annots;

target_g_annots.push_back(iter->first);

( !target_g_annots.empty() ) {

}

(

exception&) {

is_reads =

;

(track_settings.count(

) > 0)

aln_track->SetAlnType(aln_type);

}

(is_reads) {

}

(

exception&) {

aln_track->SetAnnot(iter->first);

(!iter->second.empty()) {

aln_track->SetTitle(iter->second);

aln_track->SetDSContext(ds_context);

tracks[iter->first] = aln_track.

();

sraTrack =

;

(config_num) {

config_set->

().push_back(

);

->SetLegend_text(

);

(profile ==

) {

vector<string> scoring_methods;

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

scoring_methods.push_back(

);

(config_num) {

->SetSubkey(

);

->SetSubkey(

);

enable_color = view.

(

,

);

aligned_seqfeats = view.

(

,

);

show_identical_bases = view.

(

,

);

link_mate_pair = view.

(

,

);

rendering_style = view.

(

);

show_second_pass = view.

(

,

);

flag = view.

(

, 15);

show_aln_stat = view.

(

,

);

enable_color =

;

enable_color =

;

(vector<string>, sm_iter, scoring_methods) {

scoring_method = iter->second;

unaligned_tails_mode = iter->second;

rendering_style = iter->second;

hide_sra = iter->second;

->SetHidden_settings().push_back

->SetHidden_settings().push_back

->SetHidden_settings().push_back

->SetHidden_settings().push_back

->SetHidden_settings().push_back

->SetHidden_settings().push_back

->SetHidden_settings().push_back

->SetHidden_settings().push_back

(

<<

<< iter->first <<

<< iter->second);

rendering_style =

;

,

, rendering_style,

);

choice->SetValues().push_back(

,

choice->SetValues().push_back(

,

choice->SetValues().push_back(

,

choice->SetValues().push_back(

,

->SetChoice_list().push_back(choice);

( !enable_color ) {

scoring_method =

;

,

, scoring_method,

);

(vector<string>, iter, scoring_methods) {

choice->SetValues().push_back(

*iter, *iter, *iter,

));

choice->SetValues().push_back(

,

,

,

));

->SetChoice_list().push_back(choice);

->SetCheck_boxes().push_back(

,

,

,

, link_mate_pair));

->SetCheck_boxes().push_back(

,

,

,

,

->SetCheck_boxes().push_back(

,

,

,

,

->SetCheck_boxes().push_back(

,

,

,

,

));

->SetCheck_boxes().push_back(

,

,

,

, show_identical_bases));

->SetCheck_boxes().push_back(

,

,

,

, show_second_pass, show_second_pass == view.

(

,

) ));

,

, unaligned_tails_mode,

);

choice->SetValues().push_back(

,

choice->SetValues().push_back(

,

,

choice->SetValues().push_back(

,

->SetChoice_list().push_back(choice);

(sraTrack || (

== config_num)) {

,

, hide_sra,

);

choice->SetValues().push_back(

,

choice->SetValues().push_back(

,

choice->SetValues().push_back(

,

choice->SetValues().push_back(

,

,

->SetChoice_list().push_back(choice);

,

, sort_by,

);

choice->SetValues().push_back(

,

,

,

));

->SetChoice_list().push_back(choice);

static const size_t kProjectedFeatID

static const TUnalignedTailsModeStr s_UnalignedTailsModeStrs[]

CStaticArrayMap< string, CAlignmentConfig::ELabelPosition > TLabelPosMap

static const THideSraStr s_HideSraStrs[]

static const char * kDefaultScoringMethod

static const map< string, CAlignmentTrack::ELayout > sm_LayoutMap

DEFINE_STATIC_ARRAY_MAP(TLabelPosMap, sm_LabelPosMap, s_LabelPosStrs)

static const map< CAlignmentTrack::ELayout, string > sm_LayoutDispMap

layout style to layout display name

static const TLabelPosStr s_LabelPosStrs[]

@ CONFIG_ALL

special setting for TMS tracks that did not go through complete alignment type discovery in seqconfig...

static const string kTrackName

const string & s_LayoutToDisplayName(CAlignmentTrack::ELayout layout)

static const double kMinCoverageZoomLevel

Scale at which we unconditionally switch to coverage graph.

static const int kShowPileUpRange

Range length for unconditional swith to pieup.

CStaticArrayMap< string, CAlignmentConfig::EHideSraAlignments > THideSraMap

SStaticPair< const char *, CAlignmentConfig::EUnalignedTailsMode > TUnalignedTailsModeStr

static const string kMatePairKey

static const string kGeneModelBaseKey

SStaticPair< const char *, CAlignmentConfig::ELabelPosition > TLabelPosStr

static const string kDefProfile

CSGAlignmentDS::EDataLoader s_ParseAlignDataLoader(const string &align_loader)

static const string kAlignGlyphKey

SStaticPair< const char *, CAlignmentConfig::EHideSraAlignments > THideSraStr

static const char * kDefaultUnalignedTailsMode

static const string kReadsProfile

static const size_t kContentBaseID

IAlnExplorer::EAlignType s_ParseAlignType(const string &align_type)

CStaticArrayMap< string, CAlignmentConfig::EUnalignedTailsMode > TUnalignedTailsModeMap

static const char * kDefaultSraFilter

static const string kBaseKey

void SetConfig(CConstRef< CAlignmentConfig > conf)

inline methods

static std::string const & GetHaplotypeID()

static void SetTrackSetting(objects::CChoice &choice)

static const string & GetID()

ELabelPosition m_LabelPos

@ eNormal

no compact mode

@ eExtremeCompact

extreme compact mode

CRgbaColor m_SmearColorMin

CRgbaColor m_SmearColorMax

CGlTextureFont m_LabelFont

bool m_Dirty

Dirty flag indicates any unsaved changes.

ECompactMode m_CompactMode

Alignment layout compact mode.

CRgbaColor m_UnalignedSequence

bool m_ShowIdenticalBases

bool m_ShowUnalignedTailsForTrans2GenomicAln

CRgbaColor m_NonConsensus

EUnalignedTailsMode m_UnalignedTailsMode

@ ePos_Above

above the rendered bar

@ ePos_Side

always on 5' side

virtual void RegisterIconImages() const override

virtual void GetMatchedAnnots(const TAnnotMetaDataList &src_annots, const ILayoutTrackFactory::SExtraParams &params, TAnnotNameTitleMap &out_annots) const override

virtual string GetExtensionIdentifier() const override

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual string GetExtensionLabel() const override

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual const CTrackTypeInfo & GetThisTypeInfo() const override

virtual CRef< objects::CTrackConfigSet > GetSettings(const string &profile, const TKeyValuePairs &settings, const CTempTrackProxy *track_proxy) const override

virtual TTrackMap CreateTracks(SConstScopedObject &object, ISGDataSourceContext *ds_context, CRenderingContext *r_cntx, const SExtraParams &params=SExtraParams(), const TAnnotMetaDataList &src_annots=TAnnotMetaDataList()) const override

CAlignmentTrackFactory.

static CTrackTypeInfo m_TypeInfo

void OnToggleContent(int id)

void x_OnLayoutIconClicked()

CRef< CSGAlignmentDS > m_DS

size_t m_CompactThreshold

Alignment number threshold between compact mode and non-compact mode.

void x_AddAlignmentLayout(const CSGJobResult &result)

CRef< CAlnStatConfig > m_StatConf

void x_LoadAlignmentSettings(const string &key, CRef< CAlignmentConfig > &conf)

common function for loading settings for multialign, pairwise aligns, and align smear.

int x_LayoutToCutoff(CAlignmentTrack::ELayout layout)

CAlignmentTrack.

bool m_ShowUnalignedTailsForTrans2GenomicAln

void SetAnnot(const string &annot)

virtual const CTrackTypeInfo & GetTypeInfo() const override

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const override

Initialize the HTML active area for a track.

virtual void x_OnJobCompleted(CAppJobNotification &notify) override

vector< CRef< CAlnStatGlyph > > m_StatGlyph

EAlignGlyphType x_GetAlignGlyphType(const CSeqGlyph *glyph) const

int m_MaxAlignShownFull

MaxAlignCost Show PileUp Graph is cost is higher than MaxAlignCost.

void x_OnLayoutPolicyChanged()

static ELayout LayoutStrToValue(const string &layout)

CAlignmentConfig::EHideSraAlignments m_HideSraAlignments

void x_LoadMPPWAlignSettings()

CAlignmentTrack(CSGAlignmentDS *ds, CRenderingContext *r_cntx)

size_t m_ExtremeCompactThreshold

Alignment number threshold between compact mode and extreme compact mode.

void x_SavePWAlignSettings() const

void x_AddGraphLayout(const CSGJobResult &result)

int m_MaxAlignShownAdaptive

virtual ~CAlignmentTrack()

vector< int > TSubtypeVec

virtual void x_SaveSettings(const string &preset_style) override

save part of settings to a profile string.

static const string & LayoutValueToStr(ELayout layout)

int x_LayoutToCutoff_SRA(CAlignmentTrack::ELayout layout)

CRef< CSimpleLayout > m_GeneModelLayout

CRef< CColumnLayout > m_Column

double m_MinAlignCost

MinPileUpCost - Show Coverage Graph if cost is higher than MinPileUpCost.

static CAlignmentConfig::EUnalignedTailsMode UnalignedTailsModeStrToValue(const string &tailsMode)

CRef< CBoundaryParams > m_GeneGroupConf

CRef< CHistParams > x_GetGraphParams()

void x_LoadAlignSmearSettings()

void x_OnTailsIconClicked()

CRef< CAlignmentConfig > m_MultiAlignConf

> Default Settings profile

virtual void x_OnIconClicked(TIconID id) override

Mouse left-click event handler on an icon.

void x_SaveMultiAlignSettings() const

virtual void x_UpdateBoundingBox() override

Update the bounding box assuming children's sizes are fixed if any.

static const string & HideFlagValueToStr(CAlignmentConfig::EHideSraAlignments hideSra)

static const string & LabelPosValueToStr(CAlignmentConfig::ELabelPosition pos)

void x_AddAlignStatLayout(const CSGJobResult &result)

string m_MultiAlignProfile

bool m_ShowSecondPassAlignments

IAlnExplorer::EAlignType m_AlnType

bool m_ShowAlignedSeqFeats

CRef< CAlignmentConfig > m_MPPWAlignConf

for linked pairwise aligns

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const override

Get html active areas.

void x_SaveConfiguration(const string &preset_style) const

save all track settings to the configuration file.

CAlignmentConfig::EUnalignedTailsMode m_UnalignedTailsMode

TSubtypeVec m_ProjectedFeats

virtual void x_UpdateData() override

update track content.

virtual string GetFullTitle() const override

get a more meaningful title.

string m_AlignSmearProfile

void x_AddAlignFeatLayout(CBatchJobResult &results)

void x_OnStatIconClicked()

virtual void x_LoadSettings(const string &preset_style, const TKeyValuePairs &settings) override

load the track settings.

void x_LoadAlignedSeqFeats(vector< CRef< CAlignGlyph > > &aligns, CAlignGlyph *aln)

void x_LoadMatePairSettings()

void x_SaveMatePairSettings() const

CRef< CAlignmentConfig > m_AlignSmearConf

CRef< CGeneModelConfig > m_GeneModelConfig

void x_SaveAlignSmearSettings() const

bool m_ShowIdenticalBases

static CAlignmentConfig::ELabelPosition LabelPosStrToValue(const string &pos)

void OnChangeProjectedFeats()

void x_LoadMultiAlignSettings()

void x_OnContentIconClicked()

CRef< CMatePairConfig > m_MatePairConf

void x_OnScoreIconClicked()

void x_AddAlignFeat_Recursive(CLayoutGroup::TObjectList &objs)

@ eLayout_Adaptive

adaptive using loading costs to switch between rendering modes

@ eLayout_Full

one alignment per row sorted by pos

@ eLayout_ExpandedByPos

one alignment per row sorted by pos

@ eLayout_Packed

smear/pack all alignments into one smear bar

static CAlignmentConfig::EHideSraAlignments HideFlagStrToValue(const string &hideSra)

CRef< CBoundaryParams > m_FeatGroupConf

void x_LoadPWAlignSettings()

CRef< CAlignmentConfig > m_PWAlignConf

static const string & UnalignedTailsModeValueToStr(CAlignmentConfig::EUnalignedTailsMode tailsMode)

void x_SaveAlignmentSettings(const string &key, CConstRef< CAlignmentConfig > conf) const

double m_MaxAlignCost

MinAlignCost - Show Alignment Graph if cost is higher than MinAlignCost.

wxEvtHandler * m_ContentHandler

wx-related event handler.

void x_OnChangeProjectedFeats(wxCommandEvent &)

on change the projected feature list.

void OnContextMenu(wxContextMenuEvent &anEvent)

CAlignmentTrack * m_Track

void x_OnToggleContent(wxCommandEvent &event)

CAlnContentEvtHandler(CAlignmentTrack *track)

@ fBarGraph

otherwise, shown as density table

@ fShowCount

otherwise, shown percentage

@ fShowMismatch

otherwise, shown individual count

void SetDisplayFlag(FDisplay bit, bool f)

int m_StatZoomLevel

at what zoom level to turn on statistics

void SetShowLabel(bool flag)

array< CRgbaColor, eStat_Total+1 > m_Colors

color settings

@ eStat_Mismatch

mismatches (A+G+T+C - matches)

@ eStat_Total

total alignment count at this base (A+G+T+C+Gap)

bool IsBarGraph() const

CAlnStatConfig inline method implementation.

static CRef< objects::CChoice > CreateDisplayOptions(const string &option_name, int display_flag)

CAppJobNotification Notification send by CAppJobEventTranslator.

CBatchJobResult – the data structure holding the seqgraphic job results for a batch job processing.

vector< CRef< CSGJobResult > > TResults

CColumnLayout is for creating layout by sorting glyphs into 'columns'.

void SetMinDist(TSeqPos dist)

void SetLimitRowPerGroup(bool f)

CDataTrack - a abstract base class for layout tracks which need to deal with background data retrieva...

void SetRulerType(int ruler_types)

void SetProjectedFeat(bool f)

void SetConfig(CConstRef< CFeatureParams > conf)

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

CFeatListItem - basic configuration data for one "feature" type.

CConfigurableItems - a static list of items that can be configured.

bool GetItemBySubtype(int subtype, CFeatListItem &config_item) const

void GetSelected(TFeatTypeItemSet &feat_types)

void SetSelected(TFeatTypeItemSet &feat_types)

CGeneGroup is a subclass of CLayoutGroup contains gene, RNA, cds, and Exon features.

bool m_ShowNtRuler

Show nucleotide ruler.

bool m_ShowAaRuler

Show protein ruler.

void LoadSettings(CConstRef< CSeqGraphicConfig > g_conf, const string &reg_path, const string &profile)

CRef< CCdsConfig > m_CdsConfig

virtual void x_UpdateBoundingBox()

Update the bounding box assuming children's sizes are fixed if any.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

CLayoutGroup & SetGroup()

CRef< CInlineLayout > m_Inline

const CLayoutGroup::TObjectList & GetChildren() const

const CLayoutGroup & GetGroup() const

CLayoutGroup::TObjectList & SetChildren()

CRef< CLayeredLayout > m_Layered

CRef< CSimpleLayout > m_Simple

void SetLayoutPolicy(ILayoutPolicy *policy)

Set policy on how to deploy the layout of its children.

static CGuiRegistry & GetInstance()

access the application-wide singleton

@ fNoHighlight

no highlighting on mouse over

@ fDrawBackground

highlight background for this area

@ fComment

render a label/comment on client side

@ fNoSelection

the object can't be selected

@ fTooltipEmbedded

tooltip embedded

string m_ID

area identifier

int m_Flags

area flags, will need to replace m_Type

string m_ParentId

parent entity idendifier, such as track_id

bool m_PositiveStrand

the default is true

static EScale ScaleStrToValue(const string &scale)

EScale m_Scale

requested scale

void SetDialogHost(IGlyphDialogHost *host)

void SetAnnotName(const string &name)

void SetConfig(const CSeqGraphicConfig &config)

CJobResultBase – the basic job result class holding a token.

CLayoutGroup is a container of CSeqGlyphs (layout objects).

void SetLayoutPolicy(ILayoutPolicy *policy)

Set policy on how to deploy the layout of its children.

void SetConfig(const CBoundaryParams *conf)

Set composition boundary parameters.

void PushBack(CSeqGlyph *obj)

Append a layout object to the end.

TObjectList & SetChildren()

const TObjectList & GetChildren() const

CLayoutGroup inline methods.

bool Remove(CSeqGlyph *obj)

Remove a layout object.

CConstRef< CSeqGlyph > GetChild(int idx) const

Get the layout object at index 'idx'.

void Insert(int at, CSeqGlyph *obj)

Insert a layout object before the given index.

void Set(const TObjectList &objs)

ILayoutPolicy::TObjectList TObjectList

@ eIcon_Content

icon id for setting content

@ eIcon_Layout

icon id for setting layout style

ILayoutTrackHost * m_LTHost

Top level host owning the tracks.

string GetTitle() const

get the track title.

TTrackAttrFlags m_Attrs

various track attributes

const string & GetId() const

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

@ fNavigable

Track has navigation controls.

const string & GetProfile() const

TModelUnit x_GetTBHeight() const

Get title bar height including margin.

void SetMsg(const string &msg)

static void RegisterIconImage(const TIconAlias &key, const string &img_file)

register the image for an icon.

CConstRef< CSeqGraphicConfig > x_GetGlobalConfig() const

Method for getting global configuration from rendering context.

void SetProfile(const string &preset_style)

CLayoutTrack inline method implmentation.

CRef< CSeqGraphicConfig > m_gConfig

global configuration.

int TIconID

use int as TIconID instead of EIconID.

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const

Initialize the HTML active area for a track.

void x_RegisterIcon(const SIconInfo &icon)

register track icons.

CMatePairConfig: the data structure holding alignment rendering parameters.

CRgbaColor m_FGOrientation

bool m_Dirty

Dirty flag indicates any unsaved changes.

CRgbaColor m_FGContraAlign

CRgbaColor m_SeqNonUnique

CGlTextureFont m_LabelFont

CRgbaColor m_SeqOrientation

CRgbaColor m_SeqMismatchNo

CRgbaColor m_SeqMismatchNonUnique

CRgbaColor m_SeqMismatchDistance

CRgbaColor m_SeqMismatchOrientation

TAlignList & SetSeqAligns()

vector< CRef< CAlignGlyph > > TAlignList

void SetConfig(CConstRef< CMatePairConfig > conf)

CTitleGroup is a layout group with a title.

void SetTitleFont(CGlTextureFont *font)

void SetBackgroundColor(const CRgbaColor &color)

void SetRepeatDist(int dist)

void SetRepeatTitle(bool f)

void SetTitleColor(const CRgbaColor &color)

void SetIndent(int indent)

void SetShowTitle(bool f)

class CRegistryReadView provides a nested hierarchical view at a particular key.

int GetInt(const string &key, int default_val=0) const

access a named key at this level, with no recursion

double GetReal(const string &key, double default_val=0) const

bool GetBool(const string &key, bool default_val=false) const

string GetString(const string &key, const string &default_val=kEmptyStr) const

CConstRef< objects::CUser_field > GetField(const string &key) const

provide raw field access

void Set(const string &key, int val)

access a named key at this level, with no recursion

CRenderingContext offers the basic context and utility methods for rendering layout objects in featur...

const TSeqRange & GetVisSeqRange() const

const TModelUnit & GetScale() const

TModelUnit SeqToScreen(const TModelUnit &size) const

convert from sequence positions to screen pixels

TModelUnit ScreenToSeq(const TModelUnit &size) const

convert from screen pixels to sequence positions

bool IsOverviewMode() const

bool WillSeqLetterFit() const

is it enougth space to sequence letters.

class CRgbaColor provides a simple abstraction for managing colors.

objects::CTSE_Handle m_DataHandle

void GetAnnotNames(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

const string & GetProteinScoringMethod() const

bool IsRangeCached(const TSeqRange &range) const

void SetEnableColoration(bool f)

bool GetEnableColoration() const

void SetDNAScoringMethod(const string &method)

bool GetLinkMatePairs() const

bool HasCoverageGraph() const

void SetSortBy(const string &sortby)

IAlnExplorer::EAlignType GetAlignType(const CSeqGlyph *obj) const

void LoadAlignments(const TSeqRange &range, TModelUnit window, int align_limit, bool smear_if_overlimit, TJobToken token)

void SetRemotePath(const string &remote_path)

void SetCgiMode(bool cgi_mode)

bool CanShowRange(const TSeqRange &range, int align_limit)

bool HasQualityMap() const

const string & GetSortBy() const

bool IsValidProteinScoringMethod(const string &name)

void LoadAlignFeats(const TSeqRange &range, TModelUnit window, vector< CRef< CAlignGlyph > > aligns, const vector< int > &projected_feats, TJobToken token)

void EnablePileUpCache(bool enable, bool enable_icache)

void SetLayoutPolicy(ILayoutPolicy *layout_policy)

const TMethods & GetScoringMethods(IAlnExplorer::EAlignType aln_type)

get all the existing align scoring methods.

virtual void DeleteAllJobs()

Remove waiting jobs from queue or cancel the unfinished jobs.

IAlnExplorer::EAlignType InitAlignType(bool isFastConfig=false)

This method might need object manager to connect to ID, and it is a block call.

void SetHasCoverageGraph(bool flag)

void SetUnalignedTailsMode(CAlignmentConfig::EUnalignedTailsMode tailsMode)

void SetAnnotName(const string &name)

list< CIRef< IScoringMethod > > TMethods

keep instances of score methods here.

bool IsCSRALoader() const

double GetAlignmentCost(const TSeqRange &range) const

void CalculateAlignmentScore(CSeqGlyph::TObjects &objs, TJobToken token)

void LoadCoverageGraph(const TSeqRange &range, TModelUnit window, TJobToken token)

bool IsValidDNAScoringMethod(const string &name)

double GetGraphCost(const TSeqRange &range) const

void SetHideSra(CAlignmentConfig::EHideSraAlignments hideSra)

void CalcAlnStat(const TAlnMgrVec &aligns, const TSeqRange &range, TModelUnit window, TJobToken token)

void SetMemoryLimit(Uint8 memory_limit)

vector< CConstRef< IAlnGraphicDataSource > > TAlnMgrVec

virtual void ClearJobID(TJobID job_id)

void SetProteinScoringMethod(const string &method)

void SetDataHandle(const objects::CTSE_Handle &tse)

void ResetAlnScoringJob()

const string & GetDNAScoringMethod() const

void SetShowSecondPassAlignments(bool value=true)

bool NeedReleaseMemory() const

void SetLinkMatePairs(bool f)

void SetAlnDataLoader(EDataLoader data_loader)

static const string & GetScoreName()

static CRegistryReadView GetSizeReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static void GetFont(const CRegistryReadView &view, const string &face_key, const string &size_key, CGlTextureFont &f)

static string ComposeProfileString(const TKeyValuePairs &settings)

static CRegistryReadView GetColorReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

Create a read view specifically for 'Color' section.

static CRegistryReadView GetReadView(const CGuiRegistry &reg, const string &base_key, const string &curr_key, const string &def_key1="", const string &def_key2="", const string &def_key3="")

read/readwrite view creation helper methods.

static CRegistryReadView GetLabelPosReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static CRegistryWriteView GetWriteView(CGuiRegistry &reg, const string &base_key, const string &curr_key, const string &def_key1="", const string &def_key2="", const string &def_key3="")

static CRegistryWriteView GetLabelPosRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static CRegistryWriteView GetColorRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static void ParseProfileString(const string &profile_str, TKeyValuePairs &settings)

static CRegistryWriteView GetSizeRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static void SetColor(CRegistryWriteView &view, const string &key, const CRgbaColor &color)

static void GetColor(const CRegistryReadView &view, const string &key, CRgbaColor &color)

static void SetFont(CRegistryWriteView &view, const string &face_key, const string &size_key, const CGlTextureFont &f)

static bool IsBackgroundJob()

void SetJobListener(CEventHandler *listener)

Set JobDispatcher listener.

void SetDepth(int depth)

Set the annotation selector resolving depth.

void SetAdaptive(bool flag)

void GetAnnotNames(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names, bool seq_table=false) const

CSGJobResult – the data structure holding the seqgraphic job results.

static const CFeatList * GetFeatList()

class CSeqGlyph defines an interface that wraps a rectilinear abstract object.

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

virtual void SetHeight(TModelUnit h)

void SetParent(CSeqGlyph *p)

void SetTearline(size_t Tearline)

tearline factor – used to limit a list of glyphs

virtual TModelUnit GetTop() const

virtual TModelUnit GetHeight() const

virtual void SetTop(TModelUnit b)

vector< CHTMLActiveArea > TAreaVector

list< CRef< CSeqGlyph > > TObjects

void SetRenderingContext(CRenderingContext *context)

Set the rendering context.

CRef< CHistParamsManager > GetHistParamsManager() const

Get histogram config manager.

const string & GetLabelPos() const

CRef< CGlTextureFont > GetCommentFont() const

bool GetRepeatComment() const

const string & GetSizeLevel() const

CConstRef< CFeatureParams > GetFeatParams(TFeatSubtype subtype) const

Get feature settings using a feature subtype.

const CRgbaColor & GetFGCommentColor() const

const CRgbaColor & GetBGCommentColor() const

bool GetShowComments() const

const string & GetColorTheme() const

int GetCommentRepeatDist() const

CSimpleLayout is the simpliest layout policy that simply stack a set of glyphs one on top of the othe...

@ eSort_BySeqPos

seq start position

void SetSortingType(TSortingMethod meth)

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

const string & GetSortBy() const

const CLayoutTrack * GetTrack() const

static CRef< objects::CChoice > CreateChoice(const string &name, const string &disp_name, const string &curr_val, const string &help, bool optional=false)

static CRef< objects::CHiddenSetting > CreateHiddenSetting(const string &name, const string &value)

static CRef< objects::CCheckBox > CreateCheckBox(const string &name, const string &disp_n, const string &help_text, const string &legend_txt, bool value, bool optional=false)

static CRef< objects::CChoiceItem > CreateChoiceItem(const string &name, const string &disp_name, const string &help, const string &legend_txt, bool optional=false)

CTrackTypeInfo - holds description of a layout track type.

const string & GetDescr() const

const string & GetId() const

void SetDisplay(bool is_graph)

void SetContent(bool is_agtc)

void SetValueType(bool is_count)

void SetGraphHeight(int h)

int GetGraphHeight() const

Alignment explorer interface.

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const =0

virtual bool IsColoringAvailable() const

IGlyphDialogHost An interface used for handling issues related to any dialog pops up that requires so...

virtual void PostDialogShow()=0

Post-processing after showing a dialog.

virtual void PreDialogShow()=0

Prepare for showing a dialog.

static void GetMatchedAnnots(const TAnnotMetaDataList &src_annots, const vector< string > &target_annots, const string &annot_type, const string &track_type, TAnnotNameTitleMap &out_annots)

Help function to find matched annotations.

virtual void LTH_PopupMenu(wxMenu *menu)=0

show track-specific context menu.

virtual void LTH_PushEventHandler(wxEvtHandler *handler)=0

virtual void LTH_OnLayoutChanged()=0

provides mouse coords in OpenGL viewport coord system

virtual void LTH_PopEventHandler()=0

ISGDSManager is seqgraphic data source manage that serves as an data source context.

virtual CIRef< ISGDataSource > GetDS(const string &type, SConstScopedObject &object)=0

Get a seqgraphic data source instance of the specified type.

virtual IAlnExplorer::TNumrow GetNumRows() const =0

virtual IAlnExplorer::TNumrow GetAnchor() const =0

iterator_bool insert(const value_type &val)

container_type::value_type value_type

iterator_bool insert(const value_type &val)

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

bool IsSimplified() const

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

static bool IsAlignDb(const string &annot)

check if a given annotation is AlignDb (potentially suffixed with batch identication string after a '...

static void CreateCoverageAnnotName(const string &annot_name, string &coverage_annot)

const IAlnGraphicDataSource & GetAlignMgr(void) const

Inline methods.

static bool IsGeneModelFeature(int type, int subtype)

Does feature belong to gene model track Gene, RNA, cdregion, exon, C_region, and VDJ segments.

static bool IsUnnamed(const string &annot)

check if a given annotation is a unnamed annotation.

virtual const objects::CSeq_loc & GetLocation(void) const

access the position of this object.

static TAnnotNameType NameTypeStrToValue(const string &type)

void SetConfig(const CAlignmentConfig *conf)

@ eAnnot_Other

any given named annots

IRender & GetGl()

convenience function for getting current render manager

CRef< CObject > GetResult() const

returns non-null pointer only if Completed or Running and has temporary results available

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

TRange GetTotalRange(void) const

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

TThisType & IntersectWith(const TThisType &r)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StringToBool(const CTempString str)

Convert string to bool.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static Uint8 StringToUInt8_DataSize(const CTempString str, TStringToNumFlags flags=0)

Convert string that can contain "software" qualifiers to Uint8.

static const string BoolToString(bool value)

Convert bool to string.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

void SetTo(TTo value)

Assign a value to To data member.

Tdata & Set(void)

Assign a value to data member.

E_Choice

Choice variants.

unsigned int

A callback function used to compare two keys in a database.

EVT_MENU_RANGE(MID_SHOW_TITLES, MID_HIDE_TITLES, ViewerWindowBase::OnTitleView) EVT_MENU_RANGE(MID_ENABLE_EDIT

ViewerWindowBase::OnEditMenu ViewerWindowBase::OnJustification EVT_MENU(MID_SHOW_GEOM_VLTNS, ViewerWindowBase::OnShowGeomVltns) EVT_MENU(MID_FIND_PATTERN

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

A help struct for storing information about a icon.

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

void UseDefaultMarginWidth(wxMenu &menu)

Using default menu item margin width.

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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